Align 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase (EC 5.3.1.16) (characterized)
to candidate RR42_RS18890 RR42_RS18890 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Query= reanno::BFirm:BPHYT_RS17685 (250 letters) >FitnessBrowser__Cup4G11:RR42_RS18890 Length = 248 Score = 428 bits (1100), Expect = e-125 Identities = 208/244 (85%), Positives = 230/244 (94%) Query: 1 MLLIPAIDLKDGQCVRLKQGDMDQATIFSEEPAAMARHWVDRGARRLHLVDLNGAFAGKP 60 MLLIPAIDLKDGQCVRLKQGDMDQAT+FSE+PAAMARHWV++GARRLHLVDLNGAF GKP Sbjct: 1 MLLIPAIDLKDGQCVRLKQGDMDQATVFSEDPAAMARHWVEQGARRLHLVDLNGAFVGKP 60 Query: 61 KNEDAIRAIIEEVGGEIPVQLGGGIRDLNTIERYLDDGLSYVIIGTAAVKNPGFLQDACT 120 +NE AI+AII EVG EIP+QLGGGIRDLNTIER+LD GLSYVIIGTAAVKNPGFL+DACT Sbjct: 61 RNEAAIKAIIAEVGDEIPIQLGGGIRDLNTIERWLDGGLSYVIIGTAAVKNPGFLKDACT 120 Query: 121 AFGGHIIVGLDAKDGKVATDGWSKLTGHEVADLARKFEDYGCESIIYTDIGRDGMLQGIN 180 AFGGHIIVGLDA++GKVATDGWSKLTGHEVADLARK+EDYG E+IIYTDIGRDGMLQGIN Sbjct: 121 AFGGHIIVGLDAREGKVATDGWSKLTGHEVADLARKYEDYGVEAIIYTDIGRDGMLQGIN 180 Query: 181 IEATVRLARAVKIPVIASGGLSNLTDIESLCEVEDEGIEGVICGRAIYSGDLDFAAAQTL 240 I+ATV+LA++ IPVIASGGLSNL DIE LC V+ +G+EGVICGRAIYSGDL+FA AQ L Sbjct: 181 IDATVKLAQSATIPVIASGGLSNLADIERLCSVQKDGVEGVICGRAIYSGDLNFAEAQAL 240 Query: 241 ADRL 244 AD+L Sbjct: 241 ADKL 244 Lambda K H 0.319 0.140 0.410 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 340 Number of extensions: 3 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 250 Length of database: 248 Length adjustment: 24 Effective length of query: 226 Effective length of database: 224 Effective search space: 50624 Effective search space used: 50624 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 bits)
Align candidate RR42_RS18890 RR42_RS18890 (1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase)
to HMM TIGR00007 (hisA: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase (EC 5.3.1.16))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00007.hmm # target sequence database: /tmp/gapView.5600.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00007 [M=231] Accession: TIGR00007 Description: TIGR00007: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-82 263.0 0.6 1.4e-82 262.8 0.6 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS18890 RR42_RS18890 1-(5-phosphoribosyl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS18890 RR42_RS18890 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneami # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 262.8 0.6 1.4e-82 1.4e-82 1 230 [. 3 236 .. 3 237 .. 0.97 Alignments for each domain: == domain 1 score: 262.8 bits; conditional E-value: 1.4e-82 TIGR00007 1 iiPaiDlkeGkvvrlvqGdkdkktvysddpleaakkfeeegaellHvVDLdgAkegekknlevikkive 69 +iPaiDlk+G++vrl qGd+d+ tv+s+dp+++a+++ e+ga++lH+VDL+gA+ g+++n+ +ik i+ lcl|FitnessBrowser__Cup4G11:RR42_RS18890 3 LIPAIDLKDGQCVRLKQGDMDQATVFSEDPAAMARHWVEQGARRLHLVDLNGAFVGKPRNEAAIKAIIA 71 59******************************************************************* PP TIGR00007 70 el..evkvqvGGGiRsleavekllelgverviigtaavenpelvkellkelgsekivvslDakegevav 136 e+ e+++q+GGGiR+l+++e++l+ g+++viigtaav+np ++k++ +++g +i+v+lDa+eg+va+ lcl|FitnessBrowser__Cup4G11:RR42_RS18890 72 EVgdEIPIQLGGGIRDLNTIERWLDGGLSYVIIGTAAVKNPGFLKDACTAFG-GHIIVGLDAREGKVAT 139 *9445789********************************************.99************** PP TIGR00007 137 kGWkekselslvelakkleelgleeiilTdiekdGtlsGvnveltkelvkeaeveviasGGvssiedvk 205 GW + + ++++la+k+e++g+e+ii+Tdi +dG+l+G+n+++t +l+++a+++viasGG s+ +d++ lcl|FitnessBrowser__Cup4G11:RR42_RS18890 140 DGWSKLTGHEVADLARKYEDYGVEAIIYTDIGRDGMLQGINIDATVKLAQSATIPVIASGGLSNLADIE 208 ********************************************************************* PP TIGR00007 206 alkk...lgvkgvivGkAlyegklklke 230 +l + gv+gvi+G+A+y+g+l++ e lcl|FitnessBrowser__Cup4G11:RR42_RS18890 209 RLCSvqkDGVEGVICGRAIYSGDLNFAE 236 986644499***************9877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (231 nodes) Target sequences: 1 (248 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 6.21 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory